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  • error from SOAPdenovo

    When I tried to run SOAPdenovo with a command "./SOAPdenovo all -s SB1.config -K 25 -o output", I received an error message of "-bash: ./SOAPdenovo: No such file or directory".

    Why?



    This is the content of SB1.config.

    #maximal read length
    # Lines start with '#' are ignored by the assembler
    max_rd_len=50
    [LIB]
    avg_ins=2000
    reverse_seq=1
    asm_flags=2
    rank=2
    # cutoff of pair number for a reliable connection
    #(default 5 for large insert size)
    pair_num_cutoff=5
    #minimal mapped length to contigs for a reliable read location
    #(default 35 for large insert size)
    map_len=35
    q1=/Users/Steve/bin/SOAPdenovo_1.03/SB_short.fastq
    Last edited by shuang; 07-14-2011, 08:43 AM. Reason: wrong title

  • #2
    Well, er, the obvious question first - is SOAPdenovo in your current directory?

    Confirm with ls -l SOAPdenovo

    If not you will need to refer to it by the complete path, i.e. /Users/Steve/path/to/SOAPdenovo

    Secondly, check the execute permissions are set, e.g. chmod 755 SOAPdenovo

    Hope that helps

    Comment


    • #3
      I tried all 3 things you suggested. But still getting the same error message, cannot execute binary file.

      Any other suggestions?

      Comment


      • #4
        Make sure you have downloaded the right binary for your system, check uname -a & uname -p to see. If running on Linux make sure you got the correct 32 or 64-bit versions.

        Comment


        • #5
          The problem is simply that there is no such file or directory.

          Otherwise this would happen:

          seb@fault:~/software/SOAPdenovo-PPC$ file SOAPdenovo-31mer
          SOAPdenovo-31mer: ELF 64-bit MSB executable, 64-bit PowerPC or cisco 7500, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.15, not stripped

          seb@fault:~/software/SOAPdenovo-PPC$ uname -m
          i686

          seb@fault:~/software/SOAPdenovo-PPC$ ./SOAPdenovo-31mer
          bash: ./SOAPdenovo-31mer: cannot execute binary file

          Comment


          • #6
            Seb makes a good point.

            Can you go into the directory you wish to execute SOAPdenovo from and paste the output of the following commands to this thread:

            ls -l

            uname -a

            uname -m

            file SOAPdenovo

            Comment


            • #7
              I checked my Mac. My Mac is 10.6.3. It seems eligible for the newest release 1.05, which requires Mac OS X, 10.6.5 or later.

              Thus, I downloaded Release 1.04 for Mac OS X (64 bit version, above 10.5). However, when I tried to extracted the file with this command:
              tar -zxvf SOAPdenovo-v1.04-macos-64.tgz

              However, I received this error during the process.

              grape_mac_64
              tar: A lone zero block at 521


              I also tried Mac OS X (32 bit version, above 10.5) and had similar error.

              grape_mac_32
              tar: A lone zero block at 574

              How to I fix this issue? Thanks.

              Comment

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